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PMID: 19014434 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities.

BMC microbiology ·Vol. 8 ·2008-11-11 ·Pages 195

Harrington CR, Lucchini S, Ridgway KP, Wegmann U, Eaton TJ, Hinton JC, Gasson MJ, Narbad A

Abstract

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract. We have developed a culture-independent, semi-quantitative, rapid method for detection of gut bacterial populations based on 16S rDNA probes using a DNA microarray. We compared the performance of microarrays based on long (40- and 50-mer) and short (16-21-mer) oligonucleotides. Short oligonucleotides consistently gave higher specificity. Optimal DNA amplification and labelling, hybridisation and washing conditions were determined using a probe with an increasing number of nucleotide mismatches, identifying the minimum number of nucleotides needed to distinguish between perfect and mismatch probes. An independent PCR-based control was used to normalise different hybridisation results, and to make comparisons between different samples, greatly improving the detection of changes in the gut bacterial population. The sensitivity of the microarray was determined to be 8.8 x 104 bacterial cells g-1 faecal sample, which is more sensitive than a number of existing profiling methods. The short oligonucleotide microarray was used to compare the faecal flora from healthy individuals and a patient suffering from Ulcerative Colitis (UC) during the active and remission states. Differences were identified in the bacterial profiles between healthy individuals and a UC patient. These variations were verified by Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing. In this study we demonstrate the design, testing and application of a highly sensitive, short oligonucleotide community microarray. Our approach allows the rapid discrimination of bacteria inhabiting the human GI tract, at taxonomic levels ranging from species to the superkingdom bacteria. The optimised protocol is available at: http://www.ifr.ac.uk/safety/microarrays/#protocols. It offers a high throughput method for studying the dynamics of the bacterial population over time and between individuals.

MeSH Terms
Bacteriological Techniques DNA Probes DNA, Bacterial/analysis DNA, Ribosomal/analysis Gastrointestinal Tract/microbiology Humans Molecular Sequence Data Nucleic Acid Amplification Techniques Oligonucleotide Array Sequence Analysis/methods Polymerase Chain Reaction RNA, Ribosomal, 16S/analysis,genetics Sensitivity and Specificity Sequence Analysis, DNA
Chemicals
DNA Probes DNA, Bacterial DNA, Ribosomal RNA, Ribosomal, 16S
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Harrington Carl R
Commensals and Microflora, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UA, UK. Carl.Harrington@bbsrc.ac.uk
Lucchini Sacha
Ridgway Karyn P
Wegmann Udo
Eaton Tracy J
Hinton Jay C D
Gasson Michael J
Narbad Arjan
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Article Info
Journal
BMC microbiology
Abbr.
BMC Microbiol
ISSN
1471-2180
DOI
10.1186/1471-2180-8-195
Email
carl.harrington@bbsrc.ac.uk
Published
2008-11-11
Epub
2008-00-11
Pages
195
Language
English
Region
England
NLM ID
100966981
PMCID
PMC2628385
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · 8464 · United Kingdom
External Links
PubMed source DOI: 10.1186/1471-2180-8-195 PMC Full Text View journal details
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